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ChAHP and ChAHP2 control diverse retrotransposons by complementary activities [ChIP-seq]

GSE253066 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 48 samples Submitted 2024/06/25 Platform GPL19057Platform GPL17021Platform GPL24247
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 48 samples

What it is
ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
Organism
Mus musculus (mouse)
Samples
48 samples: 23 conditions, mostly in duplicateGroups are read from the sample names, not from the paper. Check the list below.
Data you can get
A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Paper
ChAHP2 and ChAHP control diverse retrotransposons by complementary activitiesGenes & development · 2024
Summary (written by the submitters)
Retrotransposon control in mammals is an intricate process that is effectuated by a broad network of chromatin regulatory pathways. We previously discovered ChAHP, a protein complex with repressive activity against SINE retrotransposons, composed of the transcription factor ADNP, chromatin remodeler CHD4, and HP1 proteins. Here we identify ChAHP2, a protein complex homologous to ChAHP, wherein ADNP is replaced by ADNP2.
Read the full summary ↓
ChAHP2 is predominantly targeted to ERVs and LINEs, via HP1b-mediated binding of H3K9 trimethylated histones. We further demonstrate that ChAHP also binds these elements in a mechanistically equivalent manner to ChAHP2, and distinct from DNA sequence-specific recruitment at SINEs. Genetic ablation of ADNP2 alleviates ERV and LINE1 repression, which is synthetically exacerbated by additional depletion of ADNP. Together, our results reveal that the ChAHP and ChAHP2 complexes function to control both non-autonomous and autonomous retrotransposons by complementary activities, further adding to the complexity of mammalian transposon control.
Published in
ChAHP2 and ChAHP control diverse retrotransposons by complementary activities
Ahel J, Pandey A, Schwaiger M et al. · Genes & development 2024 · PMID 38960717 · doi:10.1101/gad.351769.124
This dataset
Open GSE253066 in finder → Find more mouse ChIP / ATAC / CUT&Tag datasets →
Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE253066_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA1063744 and SRA study SRP483240. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38960717) ↗
Study design
23 conditions, mostly in duplicate
Input of ChIPseq for ADNP2 in wt mES cells, ×2 Input of ChIPseq for ADNP in wt mES cells, ×2 Input of ChIPseq for ADNP in ADNP PxVxL mutan… ×2 ChIPseq for ADNP in wt mES cells, ×2 ChIPseq for ADNP in ADNP PxVxL mutant mES cel… ×2 Input of ChIPseq for H3K9me3 in untreated wt … ×2 ChIPseq for H3K9me3 in wt mES cells, ×2 ChIPseq for H3K9me3 in ADNP2 PxVxL mutant mE… ×2 +17 more

Supports a case/control comparison: 10 samples read as cases, 14 as controls.

How we read this: 23 replicated groups read from 48 sample titles; they account for 46 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study

+ 8 more — browse all 48 samples with per-sample file links →

Datasets on a similar topic

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